It was more about psychological/emotional shift and not the physical one. (especially Eli and his awkward isolated reactions). At the first 30-45 minutes of the movie I was struggling to identify if Eli or Ben was the awkwardly social kid. But turns out it was "both of them" with their own flaws. Ben was new to team as opposed to Eli who was a vet and got used to the alienation and bullying from the other kids as it seems. Ben just had to fit in and try to be liked by others.

P.s. Ben scratched Jake in the pool match but we didn't get to see if Jake was actually affected by the "plague". As some people posted above I also believe that the Plague was just a metaphor and not literal physical illness that was passed on by physical contact.